R: Write an Edge Attribute File for Cytoscape

linkcomm2cytoscape {linkcomm} | R Documentation

## Write an Edge Attribute File for Cytoscape

### Description

This function writes out an edge attribute file for visualising the link communities in Cytoscape.

### Usage

    linkcomm2cytoscape(x, interaction = "pp", ea = "temp.ea")

### Arguments

`x` | An object of class `linkcomm`.
`interaction` | A character string indicating the type of interaction between nodes. Defaults to `"pp"` for protein-protein interaction.
`ea` | A character string indicating the file for writing the edge attributes. Defaults to `"temp.ea"`.

### Details

Cytoscape is an open source platform for complex-network analysis and visualization (Shannon et al. 2003).

### Value

Used for its side-effect of writing an edge attribute file to disk.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

Shannon, P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504.

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## Write an edge attribute file to disk.
    ## Not run:
    linkcomm2cytoscape(lc)

    ## End(Not run)

[Package linkcomm version 1.0-14 Index]